Sark -
In my experience with these websites, seats are blocked for a few reasons. Sometimes, rows at the front of economy are blocked for rewards program fliers, such as Medallion on Delta.
Also (and maybe a booking agent/gate agent could confirm these) seating unaccompanied minors, those with mobility needs, or (maybe?) for staff travel? I have seen these seats boarded last on some flights, so I assume they are held until boarding is nearly complete and then released to people on standby if unused.
Also, blocks of seats could be pre-booked by travel companies for sale with their vacation packages. I guess that would depend on the destination and the time of year.